Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 139 of 144
Found at i:43063642 original size:40 final size:40
Alignment explanation
Indices: 43063569--43063702 Score: 137
Period size: 40 Copynumber: 3.4 Consensus size: 40
43063559 TTTGCAGCAT
* * * *
43063569 TTTTTAAAAAACCGCCTCTAATAG-TCGACCTATAGCGGCG
1 TTTTTAAAAAAGCGCCACTAAT-GCTTGATCTATAGCGGCG
43063609 TTTTTAAAAAAGCGCCACTAATGCTAT-ATCTATAGCGGCG
1 TTTTTAAAAAAGCGCCACTAATGCT-TGATCTATAGCGGCG
* * * * *
43063649 TTTATCAAAAGGCGCCACTAATGCTTGATTTATAGCGGCA
1 TTTTTAAAAAAGCGCCACTAATGCTTGATCTATAGCGGCG
* *
43063689 TTTTTTAGAAAGCG
1 TTTTTAAAAAAGCG
43063703 TCGCTATAGC
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
39 2 0.03
40 76 0.97
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (40 bp):
TTTTTAAAAAAGCGCCACTAATGCTTGATCTATAGCGGCG
Found at i:43063716 original size:196 final size:184
Alignment explanation
Indices: 43063376--43063829 Score: 529
Period size: 196 Copynumber: 2.4 Consensus size: 184
43063366 CGGGGTTTTC
* * * *
43063376 TTTAAAAACGCCACTAATGCTCGATCTACAGCGGCGTTTTTCAAAAAAGCGCCGCTAATGGTCGA
1 TTTAAAAACGCCACTAATG-TCGACCTATAGCGGCGTTTTT-AAAAAAGCGCCGCTAATGCTCTA
* * *
43063441 -CATATAGCAGCGTTTTTTAAAAAGCGCCACTAATGCTTGATCTATAGCGGCGTTTTTCGTAAAG
64 TC-TATAGCAGCGTTTATCAAAAAGCGCCACTAATGCTTGATCTATAGCGGCGTTTTTAGTAAAG
*
43063505 CGATGCTAAAGCCACTAAAGGTTAGCATAAAACGACGTCGTTGTGTTTAGTTTTTTTGC-AGCAT
128 CGATGCTAAAGCCACTAAAGGTCAGCATAAAACGA---C-----GTTTA-TTTTTTTGCGA-CAT
43063569 TT
183 TT
* * *
43063571 TTTAAAAAACCGCCTCTAATAGTCGACCTATAGCGGCGTTTTTAAAAAAGCGCCACTAATGCTAT
1 TTT-AAAAA-CGCCACTAAT-GTCGACCTATAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCT
* * * *
43063636 ATCTATAGCGGCGTTTATCAAAAGGCGCCACTAATGCTTGATTTATAGCGGCATTTTTTAG-AAA
63 ATCTATAGCAGCGTTTATCAAAAAGCGCCACTAATGCTTGATCTATAGCGGC-GTTTTTAGTAAA
*
43063700 GCG-TCGCTATAGCCACTAAAGGTCAGCATAAAACGACGTTTATTTTTTTGCGACATTT
127 GCGAT-GCTAAAGCCACTAAAGGTCAGCATAAAACGACGTTTATTTTTTTGCGACATTT
* * *
43063758 TTTAAAAAGCGCCGCTAATGGTCGACCTATAGTGGCGTTTTTTAAAAAGCGCCGCTAATGCTCTA
1 TTTAAAAA-CGCCACTAAT-GTCGACCTATAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCTA
43063823 TCTATAG
64 TCTATAG
43063830 GGATGTTTTT
Statistics
Matches: 229, Mismatches: 23, Indels: 23
0.83 0.08 0.08
Matches are distributed among these distances:
186 62 0.27
187 17 0.07
188 6 0.03
193 1 0.00
195 4 0.02
196 103 0.45
197 35 0.15
198 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (184 bp):
TTTAAAAACGCCACTAATGTCGACCTATAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCTATC
TATAGCAGCGTTTATCAAAAAGCGCCACTAATGCTTGATCTATAGCGGCGTTTTTAGTAAAGCGA
TGCTAAAGCCACTAAAGGTCAGCATAAAACGACGTTTATTTTTTTGCGACATTT
Found at i:43063878 original size:40 final size:39
Alignment explanation
Indices: 43063756--43063878 Score: 131
Period size: 40 Copynumber: 3.1 Consensus size: 39
43063746 TTTGCGACAT
* * * *
43063756 TTTTTAAAAAGCGCCGCTAATGGTCGACCTATAGTGGCG
1 TTTTTAAAAAGCGCCGCTAATGCTCTATCTATAGTGACG
* *
43063795 TTTTTTAAAAAGCGCCGCTAATGCTCTATCTATAGGGATG
1 -TTTTTAAAAAGCGCCGCTAATGCTCTATCTATAGTGACG
* * *
43063835 TTTTTAGGAAAGCGCCGCTAATGCT-TAATTTATAGTGCCG
1 TTTTTA-AAAAGCGCCGCTAATGCTCT-ATCTATAGTGACG
43063875 TTTT
1 TTTT
43063879 CTTTTCAAAC
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
39 7 0.10
40 63 0.90
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (39 bp):
TTTTTAAAAAGCGCCGCTAATGCTCTATCTATAGTGACG
Found at i:43066121 original size:15 final size:15
Alignment explanation
Indices: 43066085--43066123 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
43066075 AATATTATAT
43066085 TTATTATTATCATGA
1 TTATTATTATCATGA
*
43066100 TTTTTATTATCACT-A
1 TTATTATTATCA-TGA
43066115 TTATTATTA
1 TTATTATTA
43066124 CTATTACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 20 0.95
16 1 0.05
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.59
Consensus pattern (15 bp):
TTATTATTATCATGA
Found at i:43066155 original size:15 final size:14
Alignment explanation
Indices: 43066125--43066170 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
43066115 TTATTATTAC
*
43066125 TATTACTTTTATTAT
1 TATTACTTTT-CTAT
43066140 TATTACTGTTTCTAT
1 TATTACT-TTTCTAT
*
43066155 TATTGCTTTTCTAT
1 TATTACTTTTCTAT
43066169 TA
1 TA
43066171 CCATTTACGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 9 0.32
15 16 0.57
16 3 0.11
ACGTcount: A:0.22, C:0.11, G:0.04, T:0.63
Consensus pattern (14 bp):
TATTACTTTTCTAT
Found at i:43066157 original size:21 final size:21
Alignment explanation
Indices: 43066113--43066158 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
43066103 TTATTATCAC
*
43066113 TATTATTATTACTATTACTTT
1 TATTATTATTACTATTACTAT
* *
43066134 TATTATTATTACTGTTTCTAT
1 TATTATTATTACTATTACTAT
43066155 TATT
1 TATT
43066159 GCTTTTCTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.63
Consensus pattern (21 bp):
TATTATTATTACTATTACTAT
Found at i:43066167 original size:14 final size:15
Alignment explanation
Indices: 43066137--43066170 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
43066127 TTACTTTTAT
43066137 TATTATTACTGTTTC
1 TATTATTACTGTTTC
*
43066152 TATTATTGCT-TTTC
1 TATTATTACTGTTTC
43066166 TATTA
1 TATTA
43066171 CCATTTACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.62
Consensus pattern (15 bp):
TATTATTACTGTTTC
Found at i:43066223 original size:3 final size:3
Alignment explanation
Indices: 43066199--43066332 Score: 68
Period size: 3 Copynumber: 45.7 Consensus size: 3
43066189 GCACTATTCT
* * *
43066199 TTA TT- TTA TT- TTA TT- TTT TTA TTA TT- TTA TCA TTA CCTTC T-A
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA --TTA TTA
* * * * *
43066241 TTA TTG TTA TTA TTA ATA -TA CTA TTA TTA TTC TTA TTAA CGTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A -TTA TTA
* * *
43066287 TTA TTA TTA TTA TTA TTT TCTA CT- TTA TTA TTA -TA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
43066331 TT
1 TT
43066333 GCTATCATCA
Statistics
Matches: 99, Mismatches: 19, Indels: 26
0.69 0.13 0.18
Matches are distributed among these distances:
2 14 0.14
3 79 0.80
4 3 0.03
5 3 0.03
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:43066268 original size:23 final size:23
Alignment explanation
Indices: 43066238--43066301 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
43066228 TCATTACCTT
* *
43066238 CTATTATTGTTATTATTAATATA
1 CTATTATTATTATTATTAACATA
* *
43066261 CTATTATTATTCTTATTAACGTA
1 CTATTATTATTATTATTAACATA
*
43066284 TTATTATTATTATTATTA
1 CTATTATTATTATTATTA
43066302 TTTTCTACTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (23 bp):
CTATTATTATTATTATTAACATA
Found at i:43066296 original size:20 final size:20
Alignment explanation
Indices: 43066242--43066299 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
43066232 TACCTTCTAT
* *
43066242 TATTGTTATTATTAATATAC
1 TATTATTATTATTATTATAC
*
43066262 TATTATTATTCTTATTA-AC
1 TATTATTATTATTATTATAC
43066281 GTATTATTATTATTATTAT
1 -TATTATTATTATTATTAT
43066300 TATTTTCTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (20 bp):
TATTATTATTATTATTATAC
Found at i:43066419 original size:3 final size:3
Alignment explanation
Indices: 43066411--43066449 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
43066401 ATTTATTTAC
*
43066411 ATT ATT ATT GTT ATT -TCT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT
43066450 TTTAGCAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 1 0.03
3 30 0.94
4 1 0.03
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:43066855 original size:24 final size:20
Alignment explanation
Indices: 43066828--43066876 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 20
43066818 ATTTTTTAAT
43066828 TATTATTTTAAGTTATTCTATTTA
1 TATTATTTT--GTTA-TCT-TTTA
43066852 TATTATTTTGTTATCTTTTA
1 TATTATTTTGTTATCTTTTA
43066872 TATTA
1 TATTA
43066877 ATGATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.36
21 3 0.12
22 4 0.16
24 9 0.36
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (20 bp):
TATTATTTTGTTATCTTTTA
Found at i:43067460 original size:130 final size:126
Alignment explanation
Indices: 43067283--43067611 Score: 385
Period size: 130 Copynumber: 2.6 Consensus size: 126
43067273 ACGATGTTTG
* * * * *
43067283 ATGTTTAGAAATTCGAGG-AATCGTGCCCTGTCGTACTGGGTTGCAATTTCTCGTTTGTTCAAAA
1 ATGTTTGGAAATTCG-GGAAATCGTGCCCTATCGTGCTGGGTTACAATTTCCCGTTTGTTC-AAA
* * *
43067347 TGATCGAATATTCCTTTGGAATTTCACACATGTTTTAAAAATTCTTTAAAACGAAGGTAACGTTC
64 TAATCGAATATTCCTTTAGAATTTCACACATGTTTTAAAAATTC--TAAAAC-AAGGCAACGTTC
43067412 GA
126 -A
43067414 A-GTTTGGAAATTCGGGAAATCGTGCCCTATCGTGCTGGGTTACAATTTCCCGTTTGTTCAAATA
1 ATGTTTGGAAATTCGGGAAATCGTGCCCTATCGTGCTGGGTTACAATTTCCCGTTTGTTCAAATA
* ** *
43067478 ATCGAATATTCCTTTAGAATTTCACTCATGTTTTCTAAATTCTAAAACAAGGCAATGTTCA
66 ATCGAATATTCCTTTAGAATTTCACACATGTTTTAAAAATTCTAAAACAAGGCAACGTTCA
* * * * * * * ** *
43067539 ATGTTTGGGAATCCGAGAAAACGTGCCCTA-CGTGCTGGGTTTCGATTTACCGTTTGACCAAACA
1 ATGTTTGGAAATTCGGGAAATCGTGCCCTATCGTGCTGGGTTACAATTTCCCGTTTGTTCAAATA
43067603 ATCGAATAT
66 ATCGAATAT
43067612 CATTTTAAAA
Statistics
Matches: 174, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
125 39 0.22
126 34 0.20
127 6 0.03
129 44 0.25
130 50 0.29
131 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (126 bp):
ATGTTTGGAAATTCGGGAAATCGTGCCCTATCGTGCTGGGTTACAATTTCCCGTTTGTTCAAATA
ATCGAATATTCCTTTAGAATTTCACACATGTTTTAAAAATTCTAAAACAAGGCAACGTTCA
Found at i:43075423 original size:17 final size:17
Alignment explanation
Indices: 43075397--43075433 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
43075387 TTAGAAAAAC
* *
43075397 TATTCGCCATGGATAGG
1 TATTCACCATAGATAGG
43075414 TATTCACCATAGATAGG
1 TATTCACCATAGATAGG
43075431 TAT
1 TAT
43075434 CCGCCATTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (17 bp):
TATTCACCATAGATAGG
Found at i:43075440 original size:17 final size:17
Alignment explanation
Indices: 43075401--43075440 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
43075391 AAAAACTATT
* *
43075401 CGCCATGGATAGGTATT
1 CGCCATAGATAGGTATC
*
43075418 CACCATAGATAGGTATC
1 CGCCATAGATAGGTATC
43075435 CGCCAT
1 CGCCAT
43075441 TGGTATCAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (17 bp):
CGCCATAGATAGGTATC
Found at i:43076514 original size:45 final size:45
Alignment explanation
Indices: 43076382--43076594 Score: 169
Period size: 45 Copynumber: 4.7 Consensus size: 45
43076372 ACTATCAAAG
* * * *
43076382 GATGTCATAGTGTCTTTCAACTATGGTCTTAGTC-TTATTTA-CTAT
1 GATGCCATAGCGTCTTTCAGCTATGGTCTTACTCATT-TTTATC-AT
* * * ***
43076427 GATGCCATAGCGTCTTTTAGCCATAGTCTTACTCACCCTTATCAT
1 GATGCCATAGCGTCTTTCAGCTATGGTCTTACTCATTTTTATCAT
* * *
43076472 TATGCCATAGCGTCTTTCAACTATTGTCTTACTCATTTTTATCAT
1 GATGCCATAGCGTCTTTCAGCTATGGTCTTACTCATTTTTATCAT
** * * * * *
43076517 GATATCGTAGCATCTTTCAGCTATGGTCTTACTTATTATCATCAT
1 GATGCCATAGCGTCTTTCAGCTATGGTCTTACTCATTTTTATCAT
* * ** *
43076562 TATGGCATAGTATGTTTCAGCTATGGTCTTACT
1 GATGCCATAGCGTCTTTCAGCTATGGTCTTACT
43076595 TACTCCTGGT
Statistics
Matches: 132, Mismatches: 34, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
45 131 0.99
46 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.43
Consensus pattern (45 bp):
GATGCCATAGCGTCTTTCAGCTATGGTCTTACTCATTTTTATCAT
Found at i:43080705 original size:94 final size:94
Alignment explanation
Indices: 43080544--43080728 Score: 361
Period size: 94 Copynumber: 2.0 Consensus size: 94
43080534 ATAGAGGAAA
43080544 CAAAAATTAGAGATGCGGGGTATCGATCCCCATACCTCTCGCATGCTAAGCGAGCGCTCTACCAT
1 CAAAAATTAGAGATGCGGGGTATCGATCCCCATACCTCTCGCATGCTAAGCGAGCGCTCTACCAT
43080609 CTGAGCTACATCCCCTCTTCTTGTACGCT
66 CTGAGCTACATCCCCTCTTCTTGTACGCT
*
43080638 CAAAAATTGGAGATGCGGGGTATCGATCCCCATACCTCTCGCATGCTAAGCGAGCGCTCTACCAT
1 CAAAAATTAGAGATGCGGGGTATCGATCCCCATACCTCTCGCATGCTAAGCGAGCGCTCTACCAT
43080703 CTGAGCTACATCCCCTCTTCTTGTAC
66 CTGAGCTACATCCCCTCTTCTTGTAC
43080729 CCTTTTCACT
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 90 1.00
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.25
Consensus pattern (94 bp):
CAAAAATTAGAGATGCGGGGTATCGATCCCCATACCTCTCGCATGCTAAGCGAGCGCTCTACCAT
CTGAGCTACATCCCCTCTTCTTGTACGCT
Found at i:43081240 original size:7 final size:6
Alignment explanation
Indices: 43081203--43081238 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
43081193 TCTTATGTAT
*
43081203 AAAAATG AAAATG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
43081239 AGGACAAGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.06
Consensus pattern (6 bp):
AAAAAG
Found at i:43082661 original size:29 final size:29
Alignment explanation
Indices: 43082619--43082683 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
43082609 AAACATTTTA
*
43082619 AAAATGAGGTTGAGAATTTGTTTAATAAG
1 AAAATCAGGTTGAGAATTTGTTTAATAAG
43082648 AAAATCAGGTTGAGAATTTGTTTAATAAG
1 AAAATCAGGTTGAGAATTTGTTTAATAAG
43082677 AAAATCA
1 AAAATCA
43082684 AAGTGTTTCG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.45, C:0.03, G:0.20, T:0.32
Consensus pattern (29 bp):
AAAATCAGGTTGAGAATTTGTTTAATAAG
Found at i:43088066 original size:11 final size:11
Alignment explanation
Indices: 43088046--43088099 Score: 83
Period size: 11 Copynumber: 5.0 Consensus size: 11
43088036 TAGAATATAC
*
43088046 CCCATTCCTTG
1 CCCATACCTTG
43088057 CCCATACCTTG
1 CCCATACCTTG
43088068 CCCATACCTTG
1 CCCATACCTTG
*
43088079 CCCATACC-TA
1 CCCATACCTTG
43088089 CCCATACCTTG
1 CCCATACCTTG
43088100 GAAAGATCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
10 9 0.23
11 30 0.77
ACGTcount: A:0.19, C:0.46, G:0.07, T:0.28
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:43088695 original size:18 final size:18
Alignment explanation
Indices: 43088633--43088707 Score: 87
Period size: 18 Copynumber: 4.2 Consensus size: 18
43088623 TACGACCATT
*
43088633 TACGGTACTATTCACGTA
1 TACGATACTATTCACGTA
* * *
43088651 TTCAACACTATTCACGTA
1 TACGATACTATTCACGTA
*
43088669 TATGATACTATTCACGTA
1 TACGATACTATTCACGTA
* *
43088687 TACGGTACTGTTCACGTA
1 TACGATACTATTCACGTA
43088705 TAC
1 TAC
43088708 AGTAGTTGGG
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (18 bp):
TACGATACTATTCACGTA
Found at i:43092692 original size:11 final size:11
Alignment explanation
Indices: 43092672--43092714 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
43092662 TAGAATATAC
*
43092672 CCCATTCCTTG
1 CCCATACCTTG
*
43092683 CCCATACCTTT
1 CCCATACCTTG
*
43092694 CCCATACC-TA
1 CCCATACCTTG
43092704 CCCATACCTTG
1 CCCATACCTTG
43092715 GAAAGGTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.19, C:0.47, G:0.05, T:0.30
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:43093905 original size:35 final size:35
Alignment explanation
Indices: 43093858--43093950 Score: 116
Period size: 35 Copynumber: 2.7 Consensus size: 35
43093848 TAGAAAAAAA
* *
43093858 ATTGCCTTAGACGTGTCTATCTCAACCTTTTAAAG
1 ATTGCCTTAGACGAGTCTATCCCAACCTTTTAAAG
* *
43093893 ATTGCCTCAGACGAGTTTATCCCAACCTTTTAAAG
1 ATTGCCTTAGACGAGTCTATCCCAACCTTTTAAAG
* * *
43093928 GTT-CCTTAGACGGGTCTACCCCA
1 ATTGCCTTAGACGAGTCTATCCCA
43093951 TTAAGGTTGG
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 16 0.33
35 33 0.67
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (35 bp):
ATTGCCTTAGACGAGTCTATCCCAACCTTTTAAAG
Found at i:43095366 original size:3 final size:3
Alignment explanation
Indices: 43095358--43095422 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
43095348 CTTATAACGT
43095358 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
43095406 TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TA
43095423 CGTTTCTATT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:43098385 original size:21 final size:21
Alignment explanation
Indices: 43098346--43098385 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
43098336 TCTCATACGC
** *
43098346 CTGTGTGCCCATCAGACACGA
1 CTGTGTGCCCAAAACACACGA
43098367 CTGTGTGCCCAAAACACAC
1 CTGTGTGCCCAAAACACAC
43098386 ACCTATGTGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.35, G:0.20, T:0.17
Consensus pattern (21 bp):
CTGTGTGCCCAAAACACACGA
Found at i:43099571 original size:65 final size:65
Alignment explanation
Indices: 43099487--43099657 Score: 333
Period size: 65 Copynumber: 2.6 Consensus size: 65
43099477 CTAACTTTTC
*
43099487 CCCATGGCCAACAGACACGCCCGTGTGCTATGGCCGTGTGGTTCTTAACTAGCTATTGACTTAAG
1 CCCATGGCCAACAGGCACGCCCGTGTGCTATGGCCGTGTGGTTCTTAACTAGCTATTGACTTAAG
43099552 CCCATGGCCAACAGGCACGCCCGTGTGCTATGGCCGTGTGGTTCTTAACTAGCTATTGACTTAAG
1 CCCATGGCCAACAGGCACGCCCGTGTGCTATGGCCGTGTGGTTCTTAACTAGCTATTGACTTAAG
43099617 CCCATGGCCAACAGGCACGCCCGTGTGCTATGGCCGTGTGG
1 CCCATGGCCAACAGGCACGCCCGTGTGCTATGGCCGTGTGG
43099658 CACAATGCAA
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 105 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.24
Consensus pattern (65 bp):
CCCATGGCCAACAGGCACGCCCGTGTGCTATGGCCGTGTGGTTCTTAACTAGCTATTGACTTAAG
Found at i:43108485 original size:30 final size:29
Alignment explanation
Indices: 43108442--43108502 Score: 104
Period size: 30 Copynumber: 2.1 Consensus size: 29
43108432 CAAGTAGCTG
43108442 AAGCTAGTTAAATCGCACACTTAGTGCCA
1 AAGCTAGTTAAATCGCACACTTAGTGCCA
*
43108471 AAGCTAGTTTAAATCTCACACTTAGTGCCA
1 AAGCTAG-TTAAATCGCACACTTAGTGCCA
43108501 AA
1 AA
43108503 ACTTCTGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (29 bp):
AAGCTAGTTAAATCGCACACTTAGTGCCA
Found at i:43111319 original size:6 final size:6
Alignment explanation
Indices: 43111308--43111332 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
43111298 TCCTCCTTTT
43111308 TTTCTC TTTCTC TTTCTC TTTCTC T
1 TTTCTC TTTCTC TTTCTC TTTCTC T
43111333 CCTTTTATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTCTC
Found at i:43112038 original size:41 final size:36
Alignment explanation
Indices: 43111947--43112040 Score: 98
Period size: 37 Copynumber: 2.4 Consensus size: 36
43111937 CTTCTTCGAG
*
43111947 TCGATGAGGCACTGGGTGCCAATTTACTTCAGTTTA
1 TCGATGAGACACTGGGTGCCAATTTACTTCAGTTTA
* * *
43111983 ACTGAAGAGACACTGGGTGTCAATTTATTACTTCAGATTTA
1 TC-GATGAGACACTGGGTGCCAA--T-TTACTTCAG-TTTA
43112024 TTCGATGAGACACTGGG
1 -TCGATGAGACACTGGG
43112041 ACTTTGAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
36 1 0.02
37 17 0.37
39 1 0.02
40 9 0.20
41 17 0.37
42 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (36 bp):
TCGATGAGACACTGGGTGCCAATTTACTTCAGTTTA
Found at i:43114820 original size:12 final size:13
Alignment explanation
Indices: 43114798--43114832 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
43114788 CAATTCAAAT
43114798 ATTATAATAAAAA
1 ATTATAATAAAAA
*
43114811 ATTA-AATAAATA
1 ATTATAATAAAAA
43114823 ATTATAATAA
1 ATTATAATAA
43114833 TTTTTTCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
ATTATAATAAAAA
Found at i:43116432 original size:4 final size:4
Alignment explanation
Indices: 43116423--43116449 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
43116413 GGTATACAAT
43116423 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
43116450 TTCTTTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:43116968 original size:28 final size:28
Alignment explanation
Indices: 43116937--43117000 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
43116927 GGAAAAAAAA
43116937 TAAAAAATAAATAAA-GAG-AGAAGTAATG
1 TAAAAAATAAA-AAAGGAGAAGAAG-AATG
*
43116965 TAAAAGAA-AAAAAAGGAGAAGAAGAATT
1 TAAAA-AATAAAAAAGGAGAAGAAGAATG
43116993 TAAAAAAT
1 TAAAAAAT
43117001 GTTTTTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
27 5 0.16
28 19 0.61
29 7 0.23
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.16
Consensus pattern (28 bp):
TAAAAAATAAAAAAGGAGAAGAAGAATG
Found at i:43121806 original size:21 final size:21
Alignment explanation
Indices: 43121780--43121820 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
43121770 AGACGAGCAA
* *
43121780 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
43121801 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
43121821 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:43127540 original size:24 final size:24
Alignment explanation
Indices: 43127512--43127587 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
43127502 AACCTAAAGT
*
43127512 AATAAAATAAACAAGTTTAATACA
1 AATAAAATAAATAAGTTTAATACA
* * *
43127536 AAT--AATATATGAGATATTAA-AAA
1 AATAAAATAAATAAG-T-TTAATACA
*
43127559 AATAAAATAAATAAGCTTAATACA
1 AATAAAATAAATAAGTTTAATACA
43127583 AATAA
1 AATAA
43127588 TATATGTAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
22 7 0.18
23 10 0.26
24 14 0.36
25 8 0.21
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (24 bp):
AATAAAATAAATAAGTTTAATACA
Found at i:43134686 original size:13 final size:13
Alignment explanation
Indices: 43134668--43134704 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
43134658 CTCAGTAGGG
43134668 ACACGCCCGTGGC
1 ACACGCCCGTGGC
43134681 ACACGCCCGTGGC
1 ACACGCCCGTGGC
43134694 ACACGCCCGTG
1 ACACGCCCGTG
43134705 TTCGATTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.46, G:0.30, T:0.08
Consensus pattern (13 bp):
ACACGCCCGTGGC
Found at i:43140476 original size:19 final size:19
Alignment explanation
Indices: 43140452--43140489 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
43140442 GTTATCTATC
*
43140452 CAAATTTACTTTAATTATA
1 CAAATTTACCTTAATTATA
43140471 CAAATTTACCTTAATTATA
1 CAAATTTACCTTAATTATA
43140490 AAAAGTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (19 bp):
CAAATTTACCTTAATTATA
Found at i:43143115 original size:20 final size:20
Alignment explanation
Indices: 43143092--43143138 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
43143082 TTTTTTATAA
43143092 TTTTTAATATTTT-CTAATAC
1 TTTTTAATATTTTCCTAA-AC
* *
43143112 TTTTT-TTATTTTCCTAAAT
1 TTTTTAATATTTTCCTAAAC
43143131 TTTTTAAT
1 TTTTTAAT
43143139 CAATTTCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTTAATATTTTCCTAAAC
Found at i:43143154 original size:19 final size:19
Alignment explanation
Indices: 43143132--43143173 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
43143122 TTCCTAAATT
43143132 TTTTAATCAA-TTTCTTAAA
1 TTTTAA-CAATTTTCTTAAA
*
43143151 TTTTAACAATTTTTTTAAA
1 TTTTAACAATTTTCTTAAA
43143170 TTTT
1 TTTT
43143174 TTTTACAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTAACAATTTTCTTAAA
Found at i:43143249 original size:19 final size:19
Alignment explanation
Indices: 43143225--43143269 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
43143215 ATATTTCAAA
43143225 AATTTTAGT-AATT-TTTAAT
1 AATTTTA-TAAATTATTT-AT
43143244 AATTTTATAAATTATTTAT
1 AATTTTATAAATTATTTAT
43143263 AATTTTA
1 AATTTTA
43143270 CATTTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 1 0.04
19 20 0.83
20 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
AATTTTATAAATTATTTAT
Found at i:43149930 original size:22 final size:22
Alignment explanation
Indices: 43149904--43149945 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
43149894 TAAATAAATA
43149904 ATTTAAAAAAAATTAATTTAAT
1 ATTTAAAAAAAATTAATTTAAT
*
43149926 ATTTAAAATAAATTAATTTA
1 ATTTAAAAAAAATTAATTTA
43149946 CTTATTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTAAAAAAAATTAATTTAAT
Found at i:43152532 original size:51 final size:52
Alignment explanation
Indices: 43152459--43152559 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 52
43152449 GCCTAACAAT
43152459 AAAAAGGAGGGGGGGGGGGGACACCCATAATACCAGAGAATTAGTTAAATAA
1 AAAAAGGAGGGGGGGGGGGGACACCCATAATACCAGAGAATTAGTTAAATAA
43152511 AAAAAGG-GGGGGGGGGGGGACACCCATAATACCAGAGAATTAGTTAAAT
1 AAAAAGGAGGGGGGGGGGGGACACCCATAATACCAGAGAATTAGTTAAAT
43152560 TTCTTGTAGC
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 42 0.86
52 7 0.14
ACGTcount: A:0.41, C:0.12, G:0.34, T:0.14
Consensus pattern (52 bp):
AAAAAGGAGGGGGGGGGGGGACACCCATAATACCAGAGAATTAGTTAAATAA
Found at i:43156656 original size:18 final size:19
Alignment explanation
Indices: 43156620--43156658 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
43156610 TATGACAACG
43156620 AATGATATGAATGTATATA
1 AATGATATGAATGTATATA
43156639 AATGA-ATGATATGT-TATA
1 AATGATATGA-ATGTATATA
43156657 AA
1 AA
43156659 CGCTCGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (19 bp):
AATGATATGAATGTATATA
Found at i:43158537 original size:21 final size:21
Alignment explanation
Indices: 43158513--43158565 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
43158503 TTGAATTGAT
*
43158513 TCGAGTGAAATGAAATTCGAA
1 TCGAGTGAAATGAAATTCAAA
43158534 TCGAGTGAAATGAAATTCAAA
1 TCGAGTGAAATGAAATTCAAA
43158555 TCGAGTGAAAT
1 TCGAGTGAAAT
43158566 TGTTAGAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.25
Consensus pattern (21 bp):
TCGAGTGAAATGAAATTCAAA
Found at i:43158863 original size:18 final size:20
Alignment explanation
Indices: 43158842--43158883 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
43158832 AAATTTTGAA
*
43158842 AATTTTATAAA-TA-TTTTG
1 AATTTTAGAAATTATTTTTG
43158860 AATTTTAGAAATTATTTTTG
1 AATTTTAGAAATTATTTTTG
43158880 AATT
1 AATT
43158884 ATTTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
19 2 0.10
20 9 0.43
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
AATTTTAGAAATTATTTTTG
Found at i:43159739 original size:29 final size:29
Alignment explanation
Indices: 43159697--43159758 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
43159687 TGAACAGGTT
43159697 GTGTGTCTCACACGGCATTAGACACACCC
1 GTGTGTCTCACACGGCATTAGACACACCC
* * *
43159726 GTGTGTCTTACACGGTATTAGACACGCCC
1 GTGTGTCTCACACGGCATTAGACACACCC
43159755 GTGT
1 GTGT
43159759 ATCTAAGCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (29 bp):
GTGTGTCTCACACGGCATTAGACACACCC
Found at i:43163784 original size:20 final size:20
Alignment explanation
Indices: 43163761--43163800 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
43163751 TCAAATAGAA
*
43163761 GTAATGCAGTAGATGAAAAC
1 GTAATGCAGCAGATGAAAAC
43163781 GTAATGCAGCAGATGAAAAC
1 GTAATGCAGCAGATGAAAAC
43163801 ATCTTATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.25, T:0.17
Consensus pattern (20 bp):
GTAATGCAGCAGATGAAAAC
Found at i:43164023 original size:26 final size:26
Alignment explanation
Indices: 43163976--43164025 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
43163966 TTCATCATGA
* *
43163976 CACAAATTCTCAATAAATAAGTTCAT
1 CACAAATTCTCAACAAACAAGTTCAT
* *
43164002 CACAAATTCTTAACGAACAAGTTC
1 CACAAATTCTCAACAAACAAGTTC
43164026 TCCACCTCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (26 bp):
CACAAATTCTCAACAAACAAGTTCAT
Found at i:43171682 original size:42 final size:40
Alignment explanation
Indices: 43171635--43171788 Score: 155
Period size: 42 Copynumber: 3.7 Consensus size: 40
43171625 CGAGAGTATG
43171635 TGTAAGACCATATCTAGGATATGGCATCATTATGAGACTTCA
1 TGTAAGACCATATCTAGGATATGGCATCA-TATGAGA-TTCA
* *
43171677 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCG
1 TGTAAGACCATATCTAGGATATGGCATC-ATATGAGA-TTCA
* * * * * * *
43171719 TGTAAGACCATAGCTGGGCTATTGGCATGGAAACGAGATCCCA
1 TGTAAGACCATATCTAGGATA-TGGCAT-CATATGAGAT-TCA
*
43171762 TGTAAGACTATATCTAGGATATGGCAT
1 TGTAAGACCATATCTAGGATATGGCAT
43171789 TGCTGTGGTA
Statistics
Matches: 94, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
42 63 0.67
43 31 0.33
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (40 bp):
TGTAAGACCATATCTAGGATATGGCATCATATGAGATTCA
Found at i:43178239 original size:20 final size:20
Alignment explanation
Indices: 43178214--43178251 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
43178204 TTTATTTTAT
43178214 ATTTTTATATATATATTTGA
1 ATTTTTATATATATATTTGA
*
43178234 ATTTTTATATATTTATTT
1 ATTTTTATATATATATTT
43178252 TTTTAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (20 bp):
ATTTTTATATATATATTTGA
Found at i:43179447 original size:17 final size:17
Alignment explanation
Indices: 43179425--43179461 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
43179415 TAAGAAAGAA
43179425 TAATTAAAAATTTTAAT
1 TAATTAAAAATTTTAAT
**
43179442 TAATTAAATTTTTTAAT
1 TAATTAAAAATTTTAAT
43179459 TAA
1 TAA
43179462 AAATCTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAATTAAAAATTTTAAT
Found at i:43182132 original size:117 final size:120
Alignment explanation
Indices: 43181896--43182150 Score: 380
Period size: 117 Copynumber: 2.1 Consensus size: 120
43181886 TTATTAAATT
43181896 TTAATA-AGATTATTATT-AAATATAATTTAATAAAAATAAAAAGTAAATAATTTAATCATATTT
1 TTAATATA-ATTATTATTAAAATATAATTTAATAAAAATAAAAAGTAAATAATTTAATCATATTT
* *
43181959 TAACATAATTATTATTAAATACAATTTAATAAAATGATATATAATTTGAAATCATTA
65 TAACATAA-TATTATTAAATACAATTTAATAAAATAATATATAATTTGAAAACATTA
* * *
43182016 TTAATATAATTATTATTAAAATATGAA-TTAATAAAAATCATAA-TAAATAATTTAATTATATTT
1 TTAATATAATTATTATTAAAATAT-AATTTAATAAAAATAAAAAGTAAATAATTTAATCATATTT
43182079 TAACAT-A-ATTATTAAATACAATTTAATAAAATAATATATAATTT-AATAACATTA
65 TAACATAATATTATTAAATACAATTTAATAAAATAATATATAATTTGAA-AACATTA
43182133 TTAATATAATTATTATTA
1 TTAATATAATTATTATTA
43182151 TTTTAGGTAT
Statistics
Matches: 126, Mismatches: 5, Indels: 11
0.89 0.04 0.08
Matches are distributed among these distances:
116 2 0.02
117 60 0.48
119 1 0.01
120 40 0.32
121 21 0.17
122 2 0.02
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (120 bp):
TTAATATAATTATTATTAAAATATAATTTAATAAAAATAAAAAGTAAATAATTTAATCATATTTT
AACATAATATTATTAAATACAATTTAATAAAATAATATATAATTTGAAAACATTA
Found at i:43190040 original size:6 final size:5
Alignment explanation
Indices: 43190012--43190115 Score: 65
Period size: 5 Copynumber: 20.8 Consensus size: 5
43190002 TATAGTGCAT
* *
43190012 AATAA AATAA AATAA AATAA AAGTAA AAGTAA AA-AA AA-AA CA-AA AACAA
1 AATAA AATAA AATAA AATAA AA-TAA AA-TAA AATAA AATAA AATAA AATAA
* * * * *
43190061 AAAAA AACAA AAAAA CAAAAA AACAA AA-AA AATAAA AATAA AA-ATA
1 AATAA AATAA AATAA -AATAA AATAA AATAA AAT-AA AATAA AATA-A
43190107 AATAA AATA
1 AATAA AATA
43190116 TAAAACTAAA
Statistics
Matches: 86, Mismatches: 6, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
4 15 0.17
5 49 0.57
6 22 0.26
ACGTcount: A:0.83, C:0.05, G:0.02, T:0.11
Consensus pattern (5 bp):
AATAA
Found at i:43190048 original size:1 final size:1
Alignment explanation
Indices: 43190042--43190104 Score: 63
Period size: 1 Copynumber: 63.0 Consensus size: 1
43190032 AAGTAAAAGT
* * * * * * *
43190042 AAAAAAAAAACAAAAACAAAAAAAAACAAAAAAACAAAAAAACAAAAAAAATAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
43190105 TAAATAAAAT
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.89, C:0.08, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:43190056 original size:8 final size:8
Alignment explanation
Indices: 43190045--43190104 Score: 79
Period size: 8 Copynumber: 7.6 Consensus size: 8
43190035 TAAAAGTAAA
43190045 AAAAAAAC
1 AAAAAAAC
43190053 AAAAACAA-
1 AAAAA-AAC
43190061 AAAAAAAC
1 AAAAAAAC
43190069 AAAAAAAC
1 AAAAAAAC
43190077 AAAAAAAC
1 AAAAAAAC
43190085 AAAAAAA-
1 AAAAAAAC
* *
43190092 ATAAAAAT
1 AAAAAAAC
43190100 AAAAA
1 AAAAA
43190105 TAAATAAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
7 8 0.17
8 37 0.79
9 2 0.04
ACGTcount: A:0.88, C:0.08, G:0.00, T:0.03
Consensus pattern (8 bp):
AAAAAAAC
Found at i:43190062 original size:16 final size:15
Alignment explanation
Indices: 43190042--43190104 Score: 90
Period size: 16 Copynumber: 4.1 Consensus size: 15
43190032 AAGTAAAAGT
43190042 AAAAAAAAAACAAAA
1 AAAAAAAAAACAAAA
43190057 ACAAAAAAAAACAAAA
1 A-AAAAAAAAACAAAA
43190073 AAACAAAAAAACAAAA
1 AAA-AAAAAAACAAAA
* *
43190089 AAAATAAAAATAAAA
1 AAAAAAAAAACAAAA
43190104 A
1 A
43190105 TAAATAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.32
16 30 0.68
ACGTcount: A:0.89, C:0.08, G:0.00, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAACAAAA
Found at i:43190109 original size:16 final size:16
Alignment explanation
Indices: 43190015--43190126 Score: 77
Period size: 16 Copynumber: 6.9 Consensus size: 16
43190005 AGTGCATAAT
43190015 AAAAT-AAAATAAAATA
1 AAAATAAAAAT-AAATA
* * *
43190031 AAAGTAAAAGTAAAAAA
1 AAAATAAAAAT-AAATA
* * *
43190048 AAAACAAAAACAAAAA
1 AAAATAAAAATAAATA
* *
43190064 AAAACAAAAA-AACAAA
1 AAAATAAAAATAA-ATA
*
43190080 AAAACAAAAA-AAATA
1 AAAATAAAAATAAATA
43190095 AAAATAAAAATAAATA
1 AAAATAAAAATAAATA
*
43190111 AAATATAAAACTAAAT
1 AAA-ATAAAAATAAAT
43190127 GAAATCAGTT
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
15 13 0.16
16 42 0.51
17 27 0.33
ACGTcount: A:0.81, C:0.05, G:0.02, T:0.12
Consensus pattern (16 bp):
AAAATAAAAATAAATA
Found at i:43190120 original size:17 final size:17
Alignment explanation
Indices: 43190085--43190131 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
43190075 ACAAAAAAAC
43190085 AAAAA-AAATAAAA-AT
1 AAAAATAAATAAAATAT
43190100 AAAAATAAATAAAATAT
1 AAAAATAAATAAAATAT
* *
43190117 AAAACTAAATGAAAT
1 AAAAATAAATAAAAT
43190132 CAGTTGGGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 5 0.18
16 8 0.29
17 15 0.54
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (17 bp):
AAAAATAAATAAAATAT
Found at i:43202943 original size:42 final size:42
Alignment explanation
Indices: 43202879--43202964 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
43202869 TTCCTGGGTG
*
43202879 ATAATCAATAACCAGATCATAATCTTTCAGTAGCTCTAACCA
1 ATAACCAATAACCAGATCATAATCTTTCAGTAGCTCTAACCA
43202921 ATAACCAATAACCAGATCATAATCTTTCAGTAGCTCTAACCA
1 ATAACCAATAACCAGATCATAATCTTTCAGTAGCTCTAACCA
43202963 AT
1 AT
43202965 GTCATTGTCT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.28
Consensus pattern (42 bp):
ATAACCAATAACCAGATCATAATCTTTCAGTAGCTCTAACCA
Found at i:43204112 original size:26 final size:25
Alignment explanation
Indices: 43204082--43204132 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
43204072 ACAGAGGACA
43204082 TATGCCCATTTGAACAGGCCGTGTGT
1 TATGCCCATTT-AACAGGCCGTGTGT
* *
43204108 TATGCTCGTTTAACAGGCCGTGTGT
1 TATGCCCATTTAACAGGCCGTGTGT
43204133 CTCACACGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (25 bp):
TATGCCCATTTAACAGGCCGTGTGT
Found at i:43210213 original size:20 final size:20
Alignment explanation
Indices: 43210188--43210234 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
43210178 GATATGATAT
*
43210188 ACATGAT-TGAGATGATATGC
1 ACATGATATG-GATGAAATGC
*
43210208 ACATGATATGTATGAAATGC
1 ACATGATATGGATGAAATGC
43210228 ACATGAT
1 ACATGAT
43210235 GAATTCATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (20 bp):
ACATGATATGGATGAAATGC
Found at i:43210342 original size:24 final size:26
Alignment explanation
Indices: 43210284--43210342 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
43210274 GAGGAAGTGC
43210284 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
43210310 AAAAGGGCTT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
43210333 AAAAGAGGCT
1 AAAAG-GGCT
43210343 AGGCCTCCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 5 0.16
24 9 0.28
25 8 0.25
26 10 0.31
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:43210352 original size:25 final size:25
Alignment explanation
Indices: 43210284--43210352 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 25
43210274 GAGGAAGTGC
*
43210284 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGC-TAGGCCCCAGTTTATTG
**
43210310 AAAAGGGCTTTGCCCCAG-TTATT-
1 AAAAGGGCTAGGCCCCAGTTTATTG
43210333 AAAAGAGGCTAGGCCTCCAG
1 AAAAG-GGCTAGGCC-CCAG
43210353 ATATATGATA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
23 5 0.13
24 12 0.32
25 13 0.34
26 8 0.21
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.25
Consensus pattern (25 bp):
AAAAGGGCTAGGCCCCAGTTTATTG
Found at i:43215456 original size:43 final size:43
Alignment explanation
Indices: 43215326--43215461 Score: 213
Period size: 42 Copynumber: 3.2 Consensus size: 43
43215316 AAATCCCGTA
*
43215326 ATAATATCCTATAATATCCCATTAGGAATCAAATTGCTAAGAG
1 ATAATATCCTACAATATCCCATTAGGAATCAAATTGCTAAGAG
43215369 ATAATATCCTAC-ATATCCCATTAGGAATCAAATTGCTAAGAG
1 ATAATATCCTACAATATCCCATTAGGAATCAAATTGCTAAGAG
* * *
43215411 ATAATATCCTACAATATCCCATT-GAAATAAAATTGCTAAAAAG
1 ATAATATCCTACAATATCCCATTAGGAATCAAATTGCT-AAGAG
43215454 ATAATATC
1 ATAATATC
43215462 TCATAATAAT
Statistics
Matches: 87, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
42 54 0.62
43 33 0.38
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (43 bp):
ATAATATCCTACAATATCCCATTAGGAATCAAATTGCTAAGAG
Found at i:43218343 original size:22 final size:23
Alignment explanation
Indices: 43218316--43218358 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
43218306 TATAACTTTC
43218316 TTTTGGA-T-AAATATTTATAAAA
1 TTTTGGATTAAAAT-TTTATAAAA
43218338 TTTTGGATTAAAATTTTATAA
1 TTTTGGATTAAAATTTTATAA
43218359 CATAAAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 8 0.42
24 4 0.21
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (23 bp):
TTTTGGATTAAAATTTTATAAAA
Found at i:43219078 original size:23 final size:23
Alignment explanation
Indices: 43219052--43219097 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
43219042 GGTGATAAAA
* * *
43219052 GTATGCAAATGTAATAATAATAT
1 GTATACAAATGTAACAAAAATAT
*
43219075 GTATACAATTGTAACAAAAATAT
1 GTATACAAATGTAACAAAAATAT
43219098 TTAATTACTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.33
Consensus pattern (23 bp):
GTATACAAATGTAACAAAAATAT
Found at i:43220990 original size:47 final size:47
Alignment explanation
Indices: 43220889--43220992 Score: 111
Period size: 47 Copynumber: 2.2 Consensus size: 47
43220879 GCACCTTGTG
* ** * * *
43220889 TGTCGTATTGTTACTGTTACTTCGGTTTAATCCAATGAGGTACTGAG
1 TGTCGTACTGTTACTGTTACTTCGGTCAAAGCCAATGAGGCACTGAA
** *
43220936 TACCGTACTGTTACTGTTTACTTCGG-CAAAGCCGATGAGGCACTGAA
1 TGTCGTACTGTTACTG-TTACTTCGGTCAAAGCCAATGAGGCACTGAA
43220983 TGTCGTACTG
1 TGTCGTACTG
43220993 GTGTGTTGGT
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
47 36 0.80
48 9 0.20
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (47 bp):
TGTCGTACTGTTACTGTTACTTCGGTCAAAGCCAATGAGGCACTGAA
Found at i:43221490 original size:39 final size:40
Alignment explanation
Indices: 43221433--43221509 Score: 104
Period size: 39 Copynumber: 1.9 Consensus size: 40
43221423 ATTGAAAGAC
*
43221433 TAAAGTTACTGAATAACTAA-TGATTACTGAATGATTATAT
1 TAAAGTTACTGAACAACTAATTG-TTACTGAATGATTATAT
* *
43221473 TAAAG-TACTGAACAACTAATTGTTATTGATTGATTAT
1 TAAAGTTACTGAACAACTAATTGTTACTGAATGATTAT
43221510 GAATAGAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 26 0.79
40 7 0.21
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (40 bp):
TAAAGTTACTGAACAACTAATTGTTACTGAATGATTATAT
Found at i:43228071 original size:16 final size:16
Alignment explanation
Indices: 43228043--43228108 Score: 71
Period size: 16 Copynumber: 4.0 Consensus size: 16
43228033 CCATACTAAT
43228043 CATA-AATCTCATGTAA
1 CATATAATC-CATGTAA
43228059 CATATAATCCATGTAAA
1 CATATAATCCATGT-AA
*
43228076 CCTTATAATCCATGTAA
1 -CATATAATCCATGTAA
* *
43228093 CATGTAATTCATGTAA
1 CATATAATCCATGTAA
43228109 GGTATATTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
16 22 0.51
17 8 0.19
18 13 0.30
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (16 bp):
CATATAATCCATGTAA
Found at i:43228124 original size:34 final size:34
Alignment explanation
Indices: 43228051--43228132 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
43228041 ATCATAAATC
*
43228051 TCATGTAACATATAATCCATGTAAACCTTATAAT
1 TCATGTAACATGTAATCCATGTAAACCTTATAAT
* * ** *
43228085 CCATGTAACATGTAATTCATGT-AAGGTATATTAT
1 TCATGTAACATGTAATCCATGTAAACCT-TATAAT
43228119 TCATGTAACATGTA
1 TCATGTAACATGTA
43228133 CTCTATGTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
33 3 0.08
34 37 0.93
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.37
Consensus pattern (34 bp):
TCATGTAACATGTAATCCATGTAAACCTTATAAT
Found at i:43228355 original size:23 final size:23
Alignment explanation
Indices: 43228315--43228422 Score: 123
Period size: 23 Copynumber: 4.7 Consensus size: 23
43228305 AGCTGAATGA
43228315 TAAGCTCCGT-AGAGCTGAAACGG
1 TAAGCTCC-TAAGAGCTGAAACGG
* *
43228338 TAAGCCCCTAAG-GACTGAAACTG
1 TAAGCTCCTAAGAG-CTGAAACGG
*
43228361 TAAGCTCCGAAGAGCTG-AACGG
1 TAAGCTCCTAAGAGCTGAAACGG
*
43228383 TAAGCTCATAAGAGCTGAAACGG
1 TAAGCTCCTAAGAGCTGAAACGG
* *
43228406 TAAGCTCATACGAGCTG
1 TAAGCTCCTAAGAGCTG
43228423 TGGTGAGTCT
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
22 21 0.29
23 51 0.70
24 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.18
Consensus pattern (23 bp):
TAAGCTCCTAAGAGCTGAAACGG
Found at i:43228401 original size:45 final size:46
Alignment explanation
Indices: 43228291--43228412 Score: 137
Period size: 45 Copynumber: 2.7 Consensus size: 46
43228281 ACCGATAAAA
* *
43228291 GGTAAGCTCA-ATTGAGCTG-AA-TGATAAGCTCCGTAGAGCTGAAAC
1 GGTAAGCTCATA-AGAGCTGAAACTG-TAAGCTCCGAAGAGCTGAAAC
* *
43228336 GGTAAGCCCCTAAG-GACTGAAACTGTAAGCTCCGAAGAGCTG-AAC
1 GGTAAGCTCATAAGAG-CTGAAACTGTAAGCTCCGAAGAGCTGAAAC
*
43228381 GGTAAGCTCATAAGAGCTGAAACGGTAAGCTC
1 GGTAAGCTCATAAGAGCTGAAACTGTAAGCTC
43228413 ATACGAGCTG
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
44 1 0.02
45 42 0.65
46 20 0.31
47 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.19
Consensus pattern (46 bp):
GGTAAGCTCATAAGAGCTGAAACTGTAAGCTCCGAAGAGCTGAAAC
Found at i:43231400 original size:26 final size:24
Alignment explanation
Indices: 43231359--43231408 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
43231349 GTCATCACTA
* *
43231359 ACTAAAAATTAATTTATAATAATT
1 ACTAAAAAATAATTTAAAATAATT
43231383 ACTAACAAAATAACTTTAAAATAATT
1 ACTAA-AAAATAA-TTTAAAATAATT
43231409 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 6 0.27
26 11 0.50
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (24 bp):
ACTAAAAAATAATTTAAAATAATT
Found at i:43231570 original size:10 final size:10
Alignment explanation
Indices: 43231555--43231584 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
43231545 TCTACTATCC
43231555 TTTTTTCTTTT
1 TTTTTTC-TTT
43231566 TTTTTTCTTT
1 TTTTTTCTTT
43231576 TTTTTTCTT
1 TTTTTTCTT
43231585 CTCCTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.63
11 7 0.37
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:43231571 original size:11 final size:11
Alignment explanation
Indices: 43231555--43231581 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
43231545 TCTACTATCC
43231555 TTTTTTCTTTT
1 TTTTTTCTTTT
43231566 TTTTTTCTTTT
1 TTTTTTCTTTT
43231577 TTTTT
1 TTTTT
43231582 CTTCTCCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:43231712 original size:23 final size:21
Alignment explanation
Indices: 43231675--43231716 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
43231665 TTCTTCTCTT
*
43231675 CTACTTTCCTTTTTTTAAAAAA
1 CTACTTTCC-TGTTTTAAAAAA
43231697 CTACTTCTCCTGTTTTAAAA
1 CTACTT-TCCTGTTTTAAAA
43231717 CTACACAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.29, C:0.21, G:0.02, T:0.48
Consensus pattern (21 bp):
CTACTTTCCTGTTTTAAAAAA
Found at i:43232089 original size:43 final size:42
Alignment explanation
Indices: 43232013--43232098 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 42
43232003 CCTCTATCCC
43232013 TCAAACATCCTATACTCGTATCTAATTGGACATACATATTAT
1 TCAAACATCCTATACTCGTATCTAATTGGACATACATATTAT
43232055 TCAAACATCCTATACTCAGTATCTAATTGGACATACATATTAT
1 TCAAACATCCTATACTC-GTATCTAATTGGACATACATATTAT
43232098 T
1 T
43232099 TTCAAATTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 17 0.40
43 26 0.60
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (42 bp):
TCAAACATCCTATACTCGTATCTAATTGGACATACATATTAT
Found at i:43232414 original size:13 final size:13
Alignment explanation
Indices: 43232396--43232420 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43232386 AATCATGAAG
43232396 TTTCCACAATAAC
1 TTTCCACAATAAC
43232409 TTTCCACAATAA
1 TTTCCACAATAA
43232421 TCACTCTGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (13 bp):
TTTCCACAATAAC
Found at i:43238336 original size:19 final size:20
Alignment explanation
Indices: 43238312--43238350 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
43238302 TTTATGAAAA
43238312 TATTTTCTAATTT-ATTTTC
1 TATTTTCTAATTTCATTTTC
*
43238331 TATTTTCTATTTTCATTTTC
1 TATTTTCTAATTTCATTTTC
43238351 AAAAAATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.69
Consensus pattern (20 bp):
TATTTTCTAATTTCATTTTC
Found at i:43242862 original size:14 final size:14
Alignment explanation
Indices: 43242843--43242872 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
43242833 CATCTCCATG
43242843 TTTCTCTACTTTCA
1 TTTCTCTACTTTCA
43242857 TTTCTCTACTTTCA
1 TTTCTCTACTTTCA
43242871 TT
1 TT
43242873 CTCCACAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.27, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTCTCTACTTTCA
Found at i:43243228 original size:65 final size:65
Alignment explanation
Indices: 43243124--43243258 Score: 218
Period size: 65 Copynumber: 2.1 Consensus size: 65
43243114 TTTCTAACTT
*
43243124 CATTTTCATAGTCACATAGGCTATTAAACTCATAGCTTACCCTTCCATTTATTACCTTCAGTGCC
1 CATTTCCATAGTCACATAGGCTATTAAACTCATAGCTTACCCTTCCATTTATTACCTTCAGTGCC
* *
43243189 CATTTCCATAGTC-CTATAGGCTATTAAACTCATAGCTTACCCTTGCATTTATTTCCTTCAGTGC
1 CATTTCCATAGTCAC-ATAGGCTATTAAACTCATAGCTTACCCTTCCATTTATTACCTTCAGTGC
*
43243253 T
65 C
43243254 CATTT
1 CATTT
43243259 TCTAGCCCTA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
64 1 0.02
65 64 0.98
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (65 bp):
CATTTCCATAGTCACATAGGCTATTAAACTCATAGCTTACCCTTCCATTTATTACCTTCAGTGCC
Found at i:43253589 original size:156 final size:155
Alignment explanation
Indices: 43253305--43253615 Score: 595
Period size: 156 Copynumber: 2.0 Consensus size: 155
43253295 AAAGTAGTGG
43253305 TCCTAACGGGTTTCTTTTACTCATAAACTATAAAAATCTGCCAAGATAAAGAAAAAGTAAATTAA
1 TCCTAACGGGTTTCTTTTACTCATAAACTATAAAAATCTGCCAAGATAAAGAAAAAGTAAATTAA
* *
43253370 TAAATAATAAAAATAAAATAGAATTAACTTGCAAGAAAAATAAATGGCTAAAGTAATAAAAATTG
66 TAAATAATAAAAATAAAATAAAATTAAATTGCAAGAAAAATAAATGGCTAAAGTAATAAAAATTG
43253435 AGTGTTCCTAATATCTTAGTTCCCC
131 AGTGTTCCTAATATCTTAGTTCCCC
43253460 NTCCTAACGGGTTTCTTTTACTCATAAACTATAAAAATCTGCCAAGATAAAGAAAAAGTAAATTA
1 -TCCTAACGGGTTTCTTTTACTCATAAACTATAAAAATCTGCCAAGATAAAGAAAAAGTAAATTA
43253525 ATAAATAATAAAAATAAAATAAAATTAAATTGCAAGAAAAATAAATGGCTAAAGTAATAAAAATT
65 ATAAATAATAAAAATAAAATAAAATTAAATTGCAAGAAAAATAAATGGCTAAAGTAATAAAAATT
43253590 GAGTGTTCCTAATATCTTAGTTCCCC
130 GAGTGTTCCTAATATCTTAGTTCCCC
43253616 AACAACGGCG
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 153 1.00
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.29
Consensus pattern (155 bp):
TCCTAACGGGTTTCTTTTACTCATAAACTATAAAAATCTGCCAAGATAAAGAAAAAGTAAATTAA
TAAATAATAAAAATAAAATAAAATTAAATTGCAAGAAAAATAAATGGCTAAAGTAATAAAAATTG
AGTGTTCCTAATATCTTAGTTCCCC
Found at i:43258058 original size:25 final size:28
Alignment explanation
Indices: 43258024--43258078 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 28
43258014 TGTCAAAAAG
*
43258024 GAAAGAAAATGA-AA-AAGGGAG-AAAT
1 GAAAAAAAATGAGAATAAGGGAGCAAAT
*
43258049 GAAAAAAAATGAGAATATGGGAGCAAAT
1 GAAAAAAAATGAGAATAAGGGAGCAAAT
43258077 GA
1 GA
43258079 GTGGCATGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 11 0.44
26 2 0.08
27 6 0.24
28 6 0.24
ACGTcount: A:0.60, C:0.02, G:0.27, T:0.11
Consensus pattern (28 bp):
GAAAAAAAATGAGAATAAGGGAGCAAAT
Found at i:43258540 original size:11 final size:11
Alignment explanation
Indices: 43258526--43258565 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
43258516 TATTTTCTCC
43258526 CTATTTTGCTA
1 CTATTTTGCTA
*
43258537 CTATTTTACTA
1 CTATTTTGCTA
* *
43258548 TTATGTTGCTA
1 CTATTTTGCTA
43258559 CTATTTT
1 CTATTTT
43258566 ATTATTATTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.57
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:43258571 original size:22 final size:22
Alignment explanation
Indices: 43258531--43258573 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
43258521 TCTCCCTATT
43258531 TTGCTACTATTTTACTATTATG
1 TTGCTACTATTTTACTATTATG
*
43258553 TTGCTACTATTTTATTATTAT
1 TTGCTACTATTTTACTATTAT
43258574 TATTATTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.12, G:0.07, T:0.58
Consensus pattern (22 bp):
TTGCTACTATTTTACTATTATG
Found at i:43258689 original size:11 final size:11
Alignment explanation
Indices: 43258675--43258714 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
43258665 TATTTTCTCC
43258675 CTATTTTGCTA
1 CTATTTTGCTA
*
43258686 CTATTTTACTA
1 CTATTTTGCTA
* *
43258697 TTATGTTGCTA
1 CTATTTTGCTA
43258708 CTATTTT
1 CTATTTT
43258715 ATTATTATTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.57
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:43258705 original size:22 final size:22
Alignment explanation
Indices: 43258680--43258722 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
43258670 TCTCCCTATT
43258680 TTGCTACTATTTTACTATTATG
1 TTGCTACTATTTTACTATTATG
*
43258702 TTGCTACTATTTTATTATTAT
1 TTGCTACTATTTTACTATTAT
43258723 TATTATTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.12, G:0.07, T:0.58
Consensus pattern (22 bp):
TTGCTACTATTTTACTATTATG
Found at i:43258763 original size:149 final size:149
Alignment explanation
Indices: 43258515--43258812 Score: 596
Period size: 149 Copynumber: 2.0 Consensus size: 149
43258505 TATTTTCTTA
43258515 TTATTTTCTCCCTATTTTGCTACTATTTTACTATTATGTTGCTACTATTTTATTATTATTATTAT
1 TTATTTTCTCCCTATTTTGCTACTATTTTACTATTATGTTGCTACTATTTTATTATTATTATTAT
43258580 TTGAATATTATATAAAACTTATTTTATTGTTAATTTTGTTATTATTTTAAAGGCATTAGTTAATT
66 TTGAATATTATATAAAACTTATTTTATTGTTAATTTTGTTATTATTTTAAAGGCATTAGTTAATT
43258645 TTGTTATTATTTTAGAGAC
131 TTGTTATTATTTTAGAGAC
43258664 TTATTTTCTCCCTATTTTGCTACTATTTTACTATTATGTTGCTACTATTTTATTATTATTATTAT
1 TTATTTTCTCCCTATTTTGCTACTATTTTACTATTATGTTGCTACTATTTTATTATTATTATTAT
43258729 TTGAATATTATATAAAACTTATTTTATTGTTAATTTTGTTATTATTTTAAAGGCATTAGTTAATT
66 TTGAATATTATATAAAACTTATTTTATTGTTAATTTTGTTATTATTTTAAAGGCATTAGTTAATT
43258794 TTGTTATTATTTTAGAGAC
131 TTGTTATTATTTTAGAGAC
43258813 ATTTACTTAT
Statistics
Matches: 149, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 149 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (149 bp):
TTATTTTCTCCCTATTTTGCTACTATTTTACTATTATGTTGCTACTATTTTATTATTATTATTAT
TTGAATATTATATAAAACTTATTTTATTGTTAATTTTGTTATTATTTTAAAGGCATTAGTTAATT
TTGTTATTATTTTAGAGAC
Found at i:43259573 original size:13 final size:13
Alignment explanation
Indices: 43259555--43259579 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43259545 ATAAACTGTA
43259555 ATATACATACATG
1 ATATACATACATG
43259568 ATATACATACAT
1 ATATACATACAT
43259580 ATTTTAAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (13 bp):
ATATACATACATG
Found at i:43259615 original size:16 final size:16
Alignment explanation
Indices: 43259594--43259625 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
43259584 TAAACAATGC
*
43259594 TAAACATAACATACAT
1 TAAACACAACATACAT
43259610 TAAACACAACATACAT
1 TAAACACAACATACAT
43259626 ACATAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (16 bp):
TAAACACAACATACAT
Found at i:43279716 original size:24 final size:25
Alignment explanation
Indices: 43279688--43279751 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
43279678 TCAACCGAAT
* * *
43279688 TCGCACACATAGTGCTA-ATTAAGC
1 TCGCACACATAGTGCCATACTAAAC
*
43279712 TCGCACACATAATGCCATACTAAAC
1 TCGCACACATAGTGCCATACTAAAC
43279737 -CGCACACATAGTGCC
1 TCGCACACATAGTGCC
43279752 TAAAATTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 29 0.85
25 5 0.15
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.20
Consensus pattern (25 bp):
TCGCACACATAGTGCCATACTAAAC
Found at i:43279904 original size:24 final size:24
Alignment explanation
Indices: 43279877--43279978 Score: 96
Period size: 24 Copynumber: 4.0 Consensus size: 24
43279867 GAATATAAAA
*
43279877 TCTGCACACAAAGTGACTTTTAAT
1 TCTGCACACAAAGTGACATTTAAT
* * * *
43279901 TCTGCACACATAGTGCCAATCAAATAAAA
1 TCTGCACACAAAGTG---A-C-ATTTAAT
43279930 TCTGCACACAAAGTGACATTTAAT
1 TCTGCACACAAAGTGACATTTAAT
*
43279954 TCCGCACACAAAGTGACATTATAAT
1 TCTGCACACAAAGTGACATT-TAAT
43279979 AAGGCAATTT
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
24 37 0.60
25 5 0.08
26 1 0.02
27 1 0.02
28 1 0.02
29 17 0.27
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (24 bp):
TCTGCACACAAAGTGACATTTAAT
Found at i:43279980 original size:53 final size:53
Alignment explanation
Indices: 43279871--43279971 Score: 166
Period size: 53 Copynumber: 1.9 Consensus size: 53
43279861 CAAATAGAAT
* * * *
43279871 ATAAAATCTGCACACAAAGTGACTTTTAATTCTGCACACATAGTGCCAATCAA
1 ATAAAATCTGCACACAAAGTGACATTTAATTCCGCACACAAAGTGACAATCAA
43279924 ATAAAATCTGCACACAAAGTGACATTTAATTCCGCACACAAAGTGACA
1 ATAAAATCTGCACACAAAGTGACATTTAATTCCGCACACAAAGTGACA
43279972 TTATAATAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.24
Consensus pattern (53 bp):
ATAAAATCTGCACACAAAGTGACATTTAATTCCGCACACAAAGTGACAATCAA
Found at i:43296048 original size:16 final size:16
Alignment explanation
Indices: 43296027--43296058 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
43296017 GAGAATGGAG
43296027 AATAGAGACAAAGAAC
1 AATAGAGACAAAGAAC
43296043 AATAGAGACAAAGAAC
1 AATAGAGACAAAGAAC
43296059 GTTGTTGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.12, G:0.19, T:0.06
Consensus pattern (16 bp):
AATAGAGACAAAGAAC
Found at i:43298969 original size:24 final size:23
Alignment explanation
Indices: 43298913--43299029 Score: 119
Period size: 23 Copynumber: 4.9 Consensus size: 23
43298903 GACTCACCTT
*
43298913 AGCTCGTATGAGCTTACTGATATATC
1 AGCTCGTAAGAGCTTACTG-T-T-TC
43298939 AGCTCGTAAGAGCTTACTGTTCTC
1 AGCTCGTAAGAGCTTACTGTT-TC
* *
43298963 AGCTCGTATGAGCTTACTATTTC
1 AGCTCGTAAGAGCTTACTGTTTC
* * *
43298986 AGCTCATTAGAGCTTACCGTTTC
1 AGCTCGTAAGAGCTTACTGTTTC
*
43299009 AGCTC-AATAGAGCTTACTGTT
1 AGCTCGTA-AGAGCTTACTGTT
43299030 CATAGCTCGA
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
23 37 0.47
24 22 0.28
25 1 0.01
26 18 0.23
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (23 bp):
AGCTCGTAAGAGCTTACTGTTTC
Found at i:43299037 original size:47 final size:47
Alignment explanation
Indices: 43298913--43299026 Score: 133
Period size: 47 Copynumber: 2.4 Consensus size: 47
43298903 GACTCACCTT
* * * *
43298913 AGCTCGTATGAGCTTACTGATATATCAGCTCGTAAGAGCTTACTGTTCTC
1 AGCTCATATGAGCTTACT-AT-T-TCAGCTCATTAGAGCTTACCGTTCTC
*
43298963 AGCTCGTATGAGCTTACTATTTCAGCTCATTAGAGCTTACCGTT-TC
1 AGCTCATATGAGCTTACTATTTCAGCTCATTAGAGCTTACCGTTCTC
43299009 AGCTCA-ATAGAGCTTACT
1 AGCTCATAT-GAGCTTACT
43299027 GTTCATAGCT
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
45 2 0.03
46 16 0.27
47 20 0.34
48 1 0.02
49 2 0.03
50 18 0.31
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (47 bp):
AGCTCATATGAGCTTACTATTTCAGCTCATTAGAGCTTACCGTTCTC
Found at i:43299044 original size:24 final size:23
Alignment explanation
Indices: 43298913--43299044 Score: 99
Period size: 23 Copynumber: 5.5 Consensus size: 23
43298903 GACTCACCTT
* *
43298913 AGCTCGTATGAGCTTACTGATATATC
1 AGCTCGAAAGAGCTTACTG-T-T-TC
*
43298939 AGCTCGTAAGAGCTTACTGTTCTC
1 AGCTCGAAAGAGCTTACTGTT-TC
* * *
43298963 AGCTCGTATGAGCTTACTATTTC
1 AGCTCGAAAGAGCTTACTGTTTC
* *
43298986 AGCTC-ATTAGAGCTTACCGTTTC
1 AGCTCGA-AAGAGCTTACTGTTTC
43299009 AGCTC-AATAGAGCTTACTG-TTC
1 AGCTCGAA-AGAGCTTACTGTTTC
43299031 ATAGCTCGAAAGAG
1 --AGCTCGAAAGAG
43299045 TGGAAAATGA
Statistics
Matches: 90, Mismatches: 11, Indels: 12
0.80 0.10 0.11
Matches are distributed among these distances:
22 3 0.03
23 35 0.39
24 31 0.34
25 3 0.03
26 18 0.20
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (23 bp):
AGCTCGAAAGAGCTTACTGTTTC
Found at i:43300151 original size:66 final size:65
Alignment explanation
Indices: 43300029--43300156 Score: 143
Period size: 66 Copynumber: 1.9 Consensus size: 65
43300019 GGTCTCACGT
* * * * *
43300029 ACGGGCGTGTGACTGGTCGTGTGGTACAAGTCAGTATACCCCTAATTTTGGCGCACGGCCTATCG
1 ACGGGCGTGTGACTGGCCGTGTGGCACAAGTCAGTATACCCCTAAGTTT-GAGCACGACCTATCG
43300094 C
65 C
* *
43300095 ACGGGCGTGTGACTTGGCCGTGTTGCATAAGTCAGTATA-CCCTACAGGTTT-AGCACGACCTA
1 ACGGGCGTGTGAC-TGGCCGTGTGGCACAAGTCAGTATACCCCTA-A-GTTTGAGCACGACCTA
43300157 GTACACGACC
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
66 27 0.52
67 22 0.42
68 3 0.06
ACGTcount: A:0.20, C:0.25, G:0.29, T:0.26
Consensus pattern (65 bp):
ACGGGCGTGTGACTGGCCGTGTGGCACAAGTCAGTATACCCCTAAGTTTGAGCACGACCTATCGC
Found at i:43301207 original size:24 final size:24
Alignment explanation
Indices: 43301180--43301227 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
43301170 ATGTTTAAAA
*
43301180 TGTGCTGTATTACTGTTGAGAGAC
1 TGTGCTGTATCACTGTTGAGAGAC
43301204 TGTGCTGTATCACTGTTGAGAGAC
1 TGTGCTGTATCACTGTTGAGAGAC
43301228 ACTATGTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.35
Consensus pattern (24 bp):
TGTGCTGTATCACTGTTGAGAGAC
Found at i:43306769 original size:24 final size:24
Alignment explanation
Indices: 43306732--43306777 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
43306722 ACCGATATAT
*
43306732 CAGCTCGTAAGAGCTTACTGTTCC
1 CAGCTCATAAGAGCTTACTGTTCC
*
43306756 CAGCTCATATGAGCTTACTGTT
1 CAGCTCATAAGAGCTTACTGTT
43306778 TATCCGCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.33
Consensus pattern (24 bp):
CAGCTCATAAGAGCTTACTGTTCC
Found at i:43310758 original size:17 final size:17
Alignment explanation
Indices: 43310736--43310768 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
43310726 TTTAAATAAA
43310736 TAAATAAATTTCTCAAT
1 TAAATAAATTTCTCAAT
43310753 TAAATAAATTTCTCAA
1 TAAATAAATTTCTCAA
43310769 ACCAATTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATAAATTTCTCAAT
Found at i:43314324 original size:25 final size:27
Alignment explanation
Indices: 43314263--43314333 Score: 92
Period size: 26 Copynumber: 2.7 Consensus size: 27
43314253 ATATTTTCTC
43314263 AAAATTTTACTAGAGGTAAAATCATCA
1 AAAATTTTACTAGAGGTAAAATCATCA
* * *
43314290 AAAATTTTACCAG-GGTAAAATCGT-T
1 AAAATTTTACTAGAGGTAAAATCATCA
*
43314315 AAAATTTTACTAGCGGTAA
1 AAAATTTTACTAGAGGTAA
43314334 TATGGGGATG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
25 12 0.31
26 15 0.38
27 12 0.31
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (27 bp):
AAAATTTTACTAGAGGTAAAATCATCA
Found at i:43317842 original size:90 final size:90
Alignment explanation
Indices: 43317680--43317880 Score: 242
Period size: 90 Copynumber: 2.2 Consensus size: 90
43317670 TGCTTTCTAA
* * * * * * *
43317680 CCTCGAAGAGTGTGTGATCAAATAATTAAAATTTGGCTAAGTGACTTAGAAGGCTAGCATTCGAT
1 CCTCAAAGGGTGTGTGCTCAAATAATTAAAATTTGGCTAACTGACTTAAAAGGCTACCATACGAT
* * *
43317745 TTGCTATTAACTTATCAAGAAGTAC
66 CTGCTATTAACCTAGCAAGAAGTAC
* * *
43317770 CCTCAAAGGGTGTGTGCTCAAATTATTAAAATTTGGCTAACTGCCTTAAAAGGCTACCA-ACGGC
1 CCTCAAAGGGTGTGTGCTCAAATAATTAAAATTTGGCTAACTGACTTAAAAGGCTACCATAC-GA
*
43317834 TCTGCTATTAACCTAGCAAGTAGTAC
65 TCTGCTATTAACCTAGCAAGAAGTAC
*
43317860 CCTCGAAAGGGCGTGTGCTCA
1 CCTC-AAAGGGTGTGTGCTCA
43317881 TATATGAATT
Statistics
Matches: 94, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
89 1 0.01
90 78 0.83
91 15 0.16
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (90 bp):
CCTCAAAGGGTGTGTGCTCAAATAATTAAAATTTGGCTAACTGACTTAAAAGGCTACCATACGAT
CTGCTATTAACCTAGCAAGAAGTAC
Found at i:43318935 original size:14 final size:15
Alignment explanation
Indices: 43318909--43318965 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
43318899 TTTCCCAAAA
43318909 TAAATATAA-TTT-AT
1 TAAAT-TAATTTTAAT
43318923 TAAATTAATTTTAAT
1 TAAATTAATTTTAAT
43318938 T-AATTAAATTTTCAAT
1 TAAATT-AATTTT-AAT
43318954 TAAA-TAATTTTA
1 TAAATTAATTTTA
43318966 TAAACTCAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.08
14 13 0.34
15 15 0.39
16 5 0.13
17 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
TAAATTAATTTTAAT
Found at i:43321116 original size:4 final size:4
Alignment explanation
Indices: 43321107--43321173 Score: 134
Period size: 4 Copynumber: 16.8 Consensus size: 4
43321097 TTATTGTGTT
43321107 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
43321155 TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TAT
43321174 TATTTGTGAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 63 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:43328770 original size:18 final size:18
Alignment explanation
Indices: 43328747--43328793 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
43328737 TCATCAGAAC
43328747 AGCTCACCAAGAA-CTACA
1 AGCTCACCAA-AATCTACA
* *
43328765 AGCTCACTAAAATGTACA
1 AGCTCACCAAAATCTACA
43328783 AGCTCACCAAA
1 AGCTCACCAAA
43328794 TGTGTGAGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.45, C:0.30, G:0.11, T:0.15
Consensus pattern (18 bp):
AGCTCACCAAAATCTACA
Found at i:43330332 original size:24 final size:24
Alignment explanation
Indices: 43330300--43330346 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
43330290 ACACCATCAA
43330300 GTACTAAACTTGTTACAAATGTTG
1 GTACTAAACTTGTTACAAATGTTG
*
43330324 GTACTAAACTTGTTATAAATGTT
1 GTACTAAACTTGTTACAAATGTT
43330347 CTTTTAGTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (24 bp):
GTACTAAACTTGTTACAAATGTTG
Found at i:43333233 original size:17 final size:17
Alignment explanation
Indices: 43333179--43333255 Score: 77
Period size: 18 Copynumber: 4.4 Consensus size: 17
43333169 TCACCAGAAC
43333179 AGCTCACCAAGAACT-ACG
1 AGCTCACCAA-AA-TGACG
43333197 AGCTCACCAAAATGTACG
1 AGCTCACCAAAATG-ACG
43333215 AGCTCACCAAATATG-CG
1 AGCTCACCAAA-ATGACG
* * *
43333232 AGCTCACCAAGATCACA
1 AGCTCACCAAAATGACG
43333249 AGCTCAC
1 AGCTCAC
43333256 TAACACTGCG
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
16 3 0.06
17 22 0.42
18 24 0.46
19 3 0.06
ACGTcount: A:0.38, C:0.32, G:0.16, T:0.14
Consensus pattern (17 bp):
AGCTCACCAAAATGACG
Found at i:43333449 original size:3 final size:3
Alignment explanation
Indices: 43333441--43333497 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
43333431 AAGCCAAGTT
43333441 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43333489 TTA TTA TTA
1 TTA TTA TTA
43333498 GCTTATTTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:43334832 original size:5 final size:5
Alignment explanation
Indices: 43334822--43334883 Score: 124
Period size: 5 Copynumber: 12.4 Consensus size: 5
43334812 TTATGTTTTA
43334822 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
43334872 ATTAT ATTAT AT
1 ATTAT ATTAT AT
43334884 AAACTAAAGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 57 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:43336181 original size:14 final size:15
Alignment explanation
Indices: 43336140--43336173 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
43336130 CGATGAATTT
*
43336140 ATTGAATTTATATTG
1 ATTGAAATTATATTG
43336155 ATTGAAATTATATTG
1 ATTGAAATTATATTG
43336170 ATTG
1 ATTG
43336174 GATTATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (15 bp):
ATTGAAATTATATTG
Found at i:43336583 original size:23 final size:23
Alignment explanation
Indices: 43336553--43336639 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
43336543 GCTTTATCGA
* *
43336553 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
43336576 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
43336597 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
43336619 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
43336640 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:43337787 original size:14 final size:15
Alignment explanation
Indices: 43337768--43337800 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
43337758 TAGGGACAAC
*
43337768 TAAAAAT-TTTGTAT
1 TAAAAATATTTGAAT
43337782 TAAAAATATTTGAAT
1 TAAAAATATTTGAAT
43337797 TAAA
1 TAAA
43337801 CTATTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (15 bp):
TAAAAATATTTGAAT
Found at i:43338149 original size:13 final size:12
Alignment explanation
Indices: 43338114--43338152 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
43338104 TTTAATAATA
43338114 TAATAAATTA-T
1 TAATAAATTATT
43338125 TAATACAATTATT
1 TAATA-AATTATT
43338138 TCAATAAATTATT
1 T-AATAAATTATT
43338151 TA
1 TA
43338153 TTAATATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.20
12 6 0.24
13 10 0.40
14 4 0.16
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (12 bp):
TAATAAATTATT
Found at i:43340577 original size:24 final size:23
Alignment explanation
Indices: 43340549--43340605 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
43340539 TAATTTTAAA
43340549 TTTAAATAATATTCTTAAT-ATAT
1 TTTAAATAATATT-TTAATAATAT
*
43340572 TATTAAAAAATATTTTAATAATAT
1 T-TTAAATAATATTTTAATAATAT
43340596 TTT-AATAATA
1 TTTAAATAATA
43340606 AATATATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 6 0.20
23 8 0.27
24 16 0.53
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTAAATAATATTTTAATAATAT
Found at i:43340594 original size:11 final size:11
Alignment explanation
Indices: 43340548--43340605 Score: 64
Period size: 11 Copynumber: 5.1 Consensus size: 11
43340538 ATAATTTTAA
*
43340548 ATTTAAATAAT
1 ATTTTAATAAT
43340559 ATTCTTAAT-AT
1 ATT-TTAATAAT
*
43340570 ATTATTAAAAAAT
1 ATT-TT-AATAAT
43340583 ATTTTAATAAT
1 ATTTTAATAAT
43340594 ATTTTAATAAT
1 ATTTTAATAAT
43340605 A
1 A
43340606 AATATATATT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
11 27 0.68
12 8 0.20
13 5 0.12
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTTTAATAAT
Found at i:43340673 original size:18 final size:18
Alignment explanation
Indices: 43340647--43340685 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
43340637 ACAAATGTTT
*
43340647 TATAGTATAATATATTAA
1 TATAGTATAATATATAAA
* *
43340665 TATATTATACTATATAAA
1 TATAGTATAATATATAAA
43340683 TAT
1 TAT
43340686 GAATATTTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (18 bp):
TATAGTATAATATATAAA
Found at i:43341342 original size:19 final size:19
Alignment explanation
Indices: 43341318--43341354 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
43341308 AAAACAGAAT
43341318 ATGGAC-ATGTGAAATTTGC
1 ATGGACAATGT-AAATTTGC
43341337 ATGGACAATGTAAATTTG
1 ATGGACAATGTAAATTTG
43341355 TCTTTAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.32
Consensus pattern (19 bp):
ATGGACAATGTAAATTTGC
Found at i:43344847 original size:43 final size:44
Alignment explanation
Indices: 43344799--43344886 Score: 142
Period size: 43 Copynumber: 2.0 Consensus size: 44
43344789 TTTGCTGGCG
* *
43344799 TGGCTACAGGCTTGCAGTCTTTCATTCTGAATTTA-TTTAAAAT
1 TGGCTACAGGCTTGCAATCCTTCATTCTGAATTTATTTTAAAAT
*
43344842 TGGCTACATGCTTGCAATCCTTCATTCTGAATTTATTTTAAAAT
1 TGGCTACAGGCTTGCAATCCTTCATTCTGAATTTATTTTAAAAT
43344886 T
1 T
43344887 TGTTTTGCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 32 0.78
44 9 0.22
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (44 bp):
TGGCTACAGGCTTGCAATCCTTCATTCTGAATTTATTTTAAAAT
Found at i:43346001 original size:40 final size:41
Alignment explanation
Indices: 43345942--43346027 Score: 138
Period size: 40 Copynumber: 2.1 Consensus size: 41
43345932 GCAAAAATTG
*
43345942 TAAAACACAGAGCAATAGCGGCGTTTTTGGTAAAACGCCGC
1 TAAAACACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
* *
43345983 TAAAA-ACCGAGCATTAGCGGCGCTTTTGGTAAAACGCCGC
1 TAAAACACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
43346023 TAAAA
1 TAAAA
43346028 GTCATATAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 37 0.88
41 5 0.12
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (41 bp):
TAAAACACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
Found at i:43346667 original size:24 final size:24
Alignment explanation
Indices: 43346640--43346688 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
43346630 CGTATATTTG
43346640 TTAAAAGTTTATATAAAAATTAAT
1 TTAAAAGTTTATATAAAAATTAAT
43346664 TTAAAAGTTTATATAAAAATTAAT
1 TTAAAAGTTTATATAAAAATTAAT
43346688 T
1 T
43346689 GTTATTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
TTAAAAGTTTATATAAAAATTAAT
Done.